Publications

Monographs:

1. P. Formanowicz. Szeregowanie zadan w systemach z ograniczona dostepnoscia procesorow. Ph.D. thesis, Poznan University of Technology, Poznan 2000.
2. P. Formanowicz. Selected combinatorial aspects of biological sequence analysis, Publishing House of Poznan University of Technology, Poznan 2005.

Papers in journals and conference proceedings:

1997
1. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, J. Weglarz. Sequencing by Hybridization with Positive Faults. Genome Informatics 1997 , Genome Informatics Series No. 8, (S. Miyano and T. Takagi, eds.), Universal Academy Press, Tokyo, Japan, 35-42.
1998
2. J. Blazewicz, M. Drozdowski, P. Formanowicz, W. Kubiak. Szeregowanie zadan w systemach z ograniczona dostepnoscia maszyn. Zeszyty Naukowe Politechniki Slaskiej - Automatyka, z. 123, Gliwice, 1998, 55-63.
1999
3. J. Blazewicz, P. Formanowicz, F. S. Glover, M. Kasprzak. J. Weglarz. An Improved Tabu Search Algorithm for DNA Sequencing with Errors. MIC'99, Third Metaheuristics International Conference, Angra dos Reis - Rio de Janeiro, Brazil, July 19-23, 1999, 69-75.
4. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, J. Weglarz. DNA Sequencing With Positive and Negative Errors. Journal of Computational Biology Vol. 6, No. 1, 1999, 113-123.
5. J. Blazewicz, P. Formanowicz, M. Kasprzak, J. Weglarz, Informatyka a biologia obliczeniowa, Pro Dialog 8 (1999), 11-26.
6. M. L. Espinouse, P. Formanowicz, B. Penz, Minimizing the makespan in the two-machine no-wait flow-shop with limited machine availability, Computers and Industrial Engineering, 37, 1999, 497-500.
2000
7. J. Blazewicz, M. Drozdowski, P. Formanowicz, Wieslaw Kubiak, Gunter Schmidt, Scheduling preemptable tasks on parallel processors with limited availability, Parallel Computing 26, 2000, 1195-1211.
8. J. Blazewicz, P. Formanowicz, M. Kasprzak, Scheduling resumable jobs in two-machine flow shop system with limited machine availability - a constraint programming approach, Proceedings of the 2nd Workshop on Constraint Programming for Decision and Control , J. Figwer (ed.), June 27th 2000, Gliwice, Poland, 17-20.
9. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, Isothermic Oligonucleotide Libraries, in Currents in Computational Molecular Biology, Satoru Miyano, Ron Shamir, Toshihisa Takagi (eds.), Universal Academy Press, Tokyo, Japan, 2000, 97-98.
10. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, J. Weglarz, Tabu search for DNA sequencing with false negatives and false positives, European Journal of Operational Research 125, 2000, 257-265.
11. J. Blazewicz, P. Formanowicz, M. Kasprzak, P. Wierzejewski, Web Server for Computational Biology Problems, ISThmus 2000 Research and Development for the Information Society, Poznan 2000, 77-85.
12. J. Blazewicz, P. Formanowicz, W. Kubiak, M. Przysucha, G. Schmidt, Parallel branch and bound algorithms for the two-machine flow shop problem with limited machine availability, Bulletin of the Polish Academy of Sciences: Technical Sciences, 48, 2000, 105-115.
2001
13. J. Blazewicz, J. Breit, P. Formanowicz, W. Kubiak, G. Schmidt. Heuristic algorithms for the two-machine flowshop with limited machine availability. Omega - International Journal of Management Science, 29, 2001, 599-608.
14. J. Blazewicz, P. Formanowicz, M. Jaroszewski, M. Kasprzak, W. T. Markiewicz, Construction of DNA restriction maps based on a simplified experiment, Bioinformatics 17, 2001, 398-404.
15. J. Blazewicz, . Formanowicz, M. Jaroszewski, M. Kasprzak, W. T. Markiewicz, Simplified Partial Digest Method for DNA Restriction Maps Construction, in Currents in Computational Molecular Biology 2001, Nadia El-Mabrouk, Thomas Lengauer, David Sankoff (eds.), Les Publications CRM, Montreal, Canada, 2001, 9-10.
16. J. Blazewicz, P. Formanowicz, M. Kasprzak, K. Michalak, P. Wierzejewski, Clustal W algorithm for multiple sequence alignment revisited, Foundations of Computing and Decision Sciences, 26, 2001, 189-196
17. M. L. Espinouse, P. Formanowicz, B. Penz, Complexity results and approximation algorithms for the two machine no-wait flow-shop with limited machine availability, Journal of the Operational Research Society, 52, 2001, 116-121.
18. P. Formanowicz, Selected Deterministic Scheduling Problems with Limited Machine Availability, Pro Dialog, 13, 2001, 91-105.
2002
19. J. Blazewicz, P. Formanowicz, Scheduling jobs in open shops with limited machine availability, RAIRO - Operations Research 36, 2002, 149-156.
20. J. Blazewicz, P. Formanowicz, F. Guinand, M. Kasprzak, A heuristic managing errors for DNA sequencing, Bioinformatics 18, 2002, 652-660.
21. J. Blazewicz, P. Formanowicz, M. Kasprzak, D. Kobler, On the recognition of de Bruijn graphs and their induced subgraphs, Discrete Mathematics 245, 2002, 81-92.
22. J. Blazewicz, P. Formanowicz, M. Kasprzak, P. Schuurman, G. J. Woeginger, DNA sequencing, Eulerian graphs, and the exact perfect matching problem, Lecture Notes in Computer Science 2573, 2002, 13-24.
23. P. Formanowicz, Algorytmy tabu search dla problemow szeregowania zadan na jednej maszynie z ograniczona dostepnoscia, Zeszyty Naukowe Politechniki Slaskiej - seria Automatyka z. 134, Gliwice, 2002, 115-126.
24. P. Formanowicz, On Some Problems of Computational Biology, Pro Dialog, 14, 2002, 1-14.
25. W. Kubiak, J. Blazewicz, P. Formanowicz, J. Breit, G. Schmidt, Two-machine flow shops with limited machine availability, European Journal of Operational Research, 136, 2002, 528-540.
2003
26 J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Swiercz. Tabu search method for isothermic DNA sequencing by hybridization. In Currents in Computational Molecular Biology 2003, Rainer Spang, Patricia Beziat, Martin Vingron (eds.), 37-38.
27. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Swiercz. Tabu search method for DNA sequencing by hybridization with isothermic libraries. ECCB'2003 Proceedings of the European Conference on Computational Biology with conjunction with the French National Conference on Bioinformatics: "Journees Ouvertes: Biologie, Informatique, Mathematiques" (JOBIM 2003), Catherine Christophe, Hans-Peter Lenhof, Marie-France Sagot (eds.), 517-518.
28. J. Blazewicz, P. Formanowicz, R. Urbaniak. DNA Based Algorithms for Some Scheduling Problems. Lecture Notes in Computer Science 2611, 2003, 673-683.
29. M. Szachniuk, R. W. Adamiak, P. Formanowicz, Z. Gdaniec, Marta Kasprzak, Mariusz Popenda, Jacek Błażewicz. A combinatorial analysis of 2D NMR spectra of RNA duplexes. In Currents in Computational Molecular Biology 2003, Rainer Spang, Patricia Beziat, Martin Vingron (eds.), 345-346.
2004
30. R. W. Adamiak, J. Blazewicz, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, M. Szachniuk. An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes. Journal of Computational Biology 11, 2004, 163-179.
31. J. Blazewicz, M. Figlerowicz, P. Formanowicz, M. Kasprzak, B. Nowierski, R. Styszynski, Ł. Szajkowski, P. Widera, M. Wiktorczyk. Assembling the SARS-CoV genome - new method based on graph theoretical approach. Acta Biochimica Polonica 51, 2004, 983-993.
32. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz. Sequencing by hybridization with isothermic oligonucleotide libraries. Discrete Applied Mathematics 145, 2004, 40-51.
33. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, A. Swiercz. Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries. Computational Biology and Chemistry 28, 2004, 11-19.
34. J. Blazewicz, P, Formanowicz, P. Kedziora, P. Wojciechowski. Parallel algorithms for evolutionary history reconstruction. Lecture Notes in Computer Science 3019, 2004, 1138-1145.
35. P. Formanowicz. Resolving power of isithermic DNA sequencing chips. Bulletin of the Polish Academy of Sciences: Technical Sciences 52, 2004, 231-237.
2005
36. J. Blazewicz, P. Formanowicz. Multistage isothermic sequencing by hybridization. Computational Biology and Chemistry 29 (2005) 69-77.
37. J. Blazewicz, P. Formanowicz, M. Kasprzak. Selected combinatorial problems of computational biology. European Journal of Operational Research 161, 2005, 585-597.
38. C. Sadfi, B. Penz, C. Rapine, J. Blazewicz, P. Formanowicz. An improved approximation algorithm for the single machine total completion time scheduling problem with availability constraints. European Journal of Operational Research 2005, 161, 3-10.
39. A. Urbanowicz, M. Alejska, P. Formanowicz, J. Blazewicz, M. Figlerowicz, J.J. Bujarski. Homologous crossovers among molecules of brome mosaic bromovirus RNA1 or RNA2 segments in vivo. Journal of Virology 2005, 79, 5732-5742,
40. J. Blazewicz, M. Borowski, P. Formanowicz, M. Stobiecki. Tabu search method for determining sequences of amino acids in long polypeptides. Lecture Notes in Computer Science 2005, 3449, 22-32.
41. M. Figlerowicz, P. Formanowicz, P. Kedziora, M. Alejska, P. jackowiak, J. Blazewicz, W. Sluzewski, M. Figlerowicz. Znaczenie kliniczne zmian w populacji HCV w pierwszych tygodniach leczenia przewleklego zapalenia watroby typu C interferonem i rybawiryna. Przeglad Epidemiologiczny 2005, 59, 581-590.
42. P. Kedziora, M. fFiglerowicz, P. Formanowicz, M. Alejska, P. Jackowiak, N. Malinowska, A. Fratczak, j. Blazewicz, M. Figlerowicz. Computational Methods in diagnostics of chronic hepatitis C. Bulletin of the Polish Academy of Sciences: Technical Sciences 2005, 53, 273-281.

Reports

1997
1. J. Blazewicz, P. Formanowicz, M. Glowczynska, M. Kasprzak, Algorytmy wspomagajace odczytywanie genomu wykorzystujace metaheurystyke tabu search. Research report RA-5/97, Poznan Supercomputing and Networking Center, 1997.
2. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, J. Weglarz, DNA Sequencing with Positive and Negative Errors. Research report RA-002/97, Poznan Supercomputing and Networking Center, 1997.
3. W. Kubiak, J. Blazewicz, P. Formanowicz, G. Schmidt, A branch and bound algorithm for two machine flow shops with limited machine availability. Research report RA-001/97, Institute of Computing Science, Poznan University of Technology, 1997.
1998
4. J. Blazewicz, J. Breit, P. Formanowicz, W. Kubiak, G. Schmidt, Heuristics for two machine flow shops with limited machine availability, Discussion Paper B-9802, Fachbereich Wirtschaftswissenschaft, University of Saarland, 1998.
5. J. Blazewicz, M. Drozdowski, P. Formanowicz, W. Kubiak, G. Schmidt, Scheduling preemptable tasks on parallel processors with limited availability. Research report RA-005/98, Institute of Computing Science, Poznan University of Technology, 1998.
6. J. Blazewicz, P. Formanowicz, W. Kubiak, M. Przysucha, G. Schmidt, Parallel branch and bound algorithms for the flow shop problem with limited machine availability. Research report RA-4/98 Poznan Supercomputing and Networking Center, 1998.
1999
7. R. Adamiak, J. Blazewicz, P. Formanowicz, M. Kasprzak, I. Krol, M. Popenda, Analiza przestrzennej struktury RNA z wykorzystaniem algorytmow kombinatorycznych. Research report RA-2/99, Poznan Supercomputing and Networking Center, 1999.
8. J. Blazewicz, P. Formanowicz, M. Jaroszewski, M. Kasprzak, W. T. Markiewicz, Algorytmy konstruujace mapy restrykcyjne DNA, Research report RA-004/99, Poznan Supercomputing and Networking Center, Poznan 1999.
9. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. Kuroczycki, Algorytmy heurystyczne dla zagadnien sekwencjonowania z bledami, Research report RA-003/99, Poznan Supercomputing and Networking Center, Poznan 1999.
10. M.-L. Espinouse, P. Formanowicz, B. Penz, Minimizing the Makespan in the Two-Machine No-Wait Flow Shop with Limited Machine Availability. Research report No GILCO-RR-99-3 Laboratoire GILCO, Institut National Polytechnique de Grenoble, 1999.
2000
11. J. Blazewicz and P. Formanowicz, Scgeduling jobs in open shops with limited machine availability. Research report RA-004/2000, Institute of Computing Science, Poznan University of Technology, 2000.
12. J. Blazewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz, Sequencing by hybridization with isothermic oligonucleotide libraries, Research report RA-002/2000, Poznan Supercomputing and Networking Center, Poznan 2000.
13. J. Blazewicz, P. Formanowicz, M. Kasprzak, P. Wierzejewski, Serwer WWW udostepniajacy w Internecie uslugi konstrukcji drzew filogenetycznych oraz dopasowania sekwencji aminokwasowych URL:http://cbs.cs.put.poznan.pl/, Research report RA-005/2000, Poznan Supercomputing and Networking Center, Poznan 2000.
2003
14. J. Blazewicz, P. Formanowicz, P. Kedziora, P. Wojciechowski. Parallel implementation of algorithms for evolutionary history reconstruction on SUN Fire 6800 computer. Research Report RA-004/2003 of Poznan Supercomputing and Networking Center.
15. P. Formanowicz, S. Gawiejnowicz. Single machine scheduling with periods of machine non-availability of variable lengths. Research Report RA-011/03, Institute of Computing Science, Poznan University of Technology, Poznan 2003.
16. P. Formanowicz, K. Kwarciak. Zastosowanie teorii jezykow formalnych do wykrywania genow kodujacych RNA. Raport RB-038/03 Instytutu Informatyki Politechniki Poznanskiej, Poznan 2003.


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Last modified: Dec 09, 2005